Is the market really falling to gba levels when the gba was not given a proper lifespan and probably would have hit over a hundred million with the 4.5 years the 3DS will have at least before a successor. And is it really healthy for nintendo when they are investing so much more money into handheld games and that sector is making up a large part of the profit margin
That's all part of generational transitions - they aren't fixed in rigid timelines. That's similar to people who get all excited that the PS3/360 (64M in the US) have sold so well compared to PS2/XBX (60M in the US), without highlighting that the PS3/360 have had 15 years on the market before their successors hit vs. 10 years for PS2/XBX. That's a much more extreme example, but that's how the generation played out.
In any case, Nintendo shipped the GBA for 10 fiscal years (albeit small numbers the last couple years), and it kept selling very well in the US following the release of the DS. But yeah, the GBA would have put up somewhat bigger numbers in the US if it had another year to itself. But the GBA was already slowing down by mid-2004 in Japan, so I'm not sure it would have made a big difference there. So yeah, the 3DS should have an extra year (maybe even two) to itself before a successor, but the overall length of the 3DS lifespan should be similar to the GBA, and when you actually look back at the GBA sales post-DS, I really don't think they were hurt as much as you might think. The GBC sold 19M units the year the GBA released, and only 4.7M the year after. Likewise, the DS sold 17.5M units the year the 3DS released, and only 5.1M the year after. But the GBA sold 15.4M units the year the DS released, and still sold another 8.3M units the year after. Not at all a typical drop-off following the release of a successor.
Regardless, I suspect it will fall a bit further behind the GBA over the next year or two, and then start outselling the GBA in the latter years of its life - but for the sake of this argument, it really only needs like 75M or so (and I think 80M+ is pretty much a lock), and maybe even less if Sony can revive the Vita and push out more than 10M+ of that.
Is it healthy for Nintendo? Well, it's obviously not nearly as good as what they did with the DS, but that was lightning in a bottle. It wasn't going to happen again - and you can't build your business around counting on anomalies to happen repeatedly.
But the GBA/GC situation doesn't need to be all that different from the 3DS/WiiU situation (although it may turn out that way if Nintendo can't get the WiiU up to GC levels - but that's not the point). It's a situation where Nintendo can still make money (as long as they don't bleed due to the WiiU). The 3DS hardware has the potential of being more profitable than the GBA (they just weren't making much money on $99/$79 GBA prices), some of the premium games sell for a higher price, there's E-Shop + Virtual Console + DLC, etc. That all helps to offset the larger development budgets.
Anyway, long-winded answer to what was probably intended to be a simple question. But Nintendo was just fine with GBA level sales with a home console that failed.
Shifting the topic somewhat, but I'll go ahead and say that this past home console generation was artificially inflated (historically speaking) as well, much like the handheld generation. And I suspect we'll see a pretty severe drop-off back to previous generation standards with this new generation. This generation had the Wii tapping into an entirely new demographic, the 360 elevated itself mid-gen thanks to the Kinect, the generation lasted longer than I suspect the new generation will last (somebody will release a new system before 2020 - or else there just won't be anymore traditional consoles), and PC gaming was at its nadir around the start of the previous generation, whereas PC gaming is a much stronger player again this time.
This current gen will finish up somewhere not far from 300M. I could totally see the upcoming gen falling back close to the ~200M from the previous gen, or maybe even edging down closer to the 150M from the gen before that.